Actually, I don't think the Green/Blue/Red endings are that much of a problem for setting up a sequel. If ME4 takes place hundreds of years after ME3, then the only choices that will have long lasting repercusions would be the genophage and the krogans, the quarians and the geth, and the ending choice.
About the ending choice, if the events of ME4 are separated from the events of ME3 by a wide time margin, then they could brush aside most of the differences between them. For example, in a Synthesis scenerario, they could have people on the galaxy having a bit of a greenish glow to them (but toned down compared to ME3) and make some offhand references about the new cooperation between organic/synthetic hybrids. They could also have the Reapers retire to live alone and not get involved with the rest of the galaxy's affairs, so they would only have cameo appearances. Apart from that, there wouldn't be much to tell that we are dealing with a post-Synthesis galaxy.
Similarly, in Good Destroy and Control scenerios, the differences would be minimal. The big difference between these scenarios would be that in Control, the Reapers and Shepard are still alive, but they chose (like in Synthesis) to retire and live alone, so they would only make cameo appearances.
I think the outcome of the Tuchanka and Rannoch arcs have more visible and obvious impacts on the galaxy than the ending choices. That said, there aren't that many variables in the resolution to the Tuchanka and Rannoch arcs, so I think they could probably work that out into the next game, but it's definitely getting trickier at this point (and I'm not sure they could pull it off).
The variables that I think kind of fuck up the setting for ME4 are the variations of the Destroy ending. The Bad Destroy ending involves the near (if not outright) extinction of several species on the galaxy. Unless they decide the Bad Destroy ending is non-canon (like the Refusal ending), I can't see how they could work that out into the next game.